Starting phenix.real_space_refine
on Thu Mar  6 05:04:50 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/7pag_13269/03_2025/7pag_13269.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pag_13269/03_2025/7pag_13269.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pag_13269/03_2025/7pag_13269.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pag_13269/03_2025/7pag_13269.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pag_13269/03_2025/7pag_13269.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pag_13269/03_2025/7pag_13269.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 971 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      3      9.91       5
     S      28      5.16       5
     C    2504      2.51       5
     N     746      2.21       5
     O     759      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4040
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4023
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 509, 4023
          Classifications: {'peptide': 509}
          Link IDs: {'PTRANS': 23, 'TRANS': 485}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 17
          Unusual residues: {' CA': 3, 'NAG': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 3.20, per 1000 atoms: 0.79
  Number of scatterers: 4040
  At special positions: 0
  Unit cell: (91.12, 71.02, 171.52, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      3     19.99
     S      28     16.00
     O     759      8.00
     N     746      7.00
     C    2504      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  75 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  30 " - pdb=" SG  CYS A  72 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 241 " - pdb=" SG  CYS A 407 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 256 " - pdb=" SG  CYS A 278 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 376 " - pdb=" SG  CYS A 392 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 380 " - pdb=" SG  CYS A 394 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 396 " - pdb=" SG  CYS A 406 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 496 " - pdb=" SG  CYS A 509 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 524 " - pdb=" SG  CYS A 533 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 604 " - " ASN A 204 "
  Time building additional restraints: 1.61
  Conformation dependent library (CDL) restraints added in 546.6 milliseconds
  

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  956

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 6 sheets defined
      15.1% alpha, 54.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 39 through 43
    Processing helix  chain 'A' and resid 189 through 199
    Processing helix  chain 'A' and resid 204 through 219
      removed outlier: 4.372A  pdb=" N   HIS A 209 " --> pdb=" O   SER A 205 " (cutoff:3.500A)
      removed outlier: 4.820A  pdb=" N   ALA A 210 " --> pdb=" O   SER A 206 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   SER A 217 " --> pdb=" O   ARG A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 312
    Processing helix  chain 'A' and resid 320 through 331
      removed outlier: 3.726A  pdb=" N   PHE A 324 " --> pdb=" O   THR A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 334
      No H-bonds generated for 'chain 'A' and resid 332 through 334'
    Processing helix  chain 'A' and resid 346 through 349
    Processing helix  chain 'A' and resid 353 through 355
      No H-bonds generated for 'chain 'A' and resid 353 through 355'
    Processing helix  chain 'A' and resid 356 through 373
      removed outlier: 3.773A  pdb=" N   GLN A 361 " --> pdb=" O   GLU A 357 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   ALA A 362 " --> pdb=" O   ALA A 358 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ILE A 363 " --> pdb=" O   LEU A 359 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   TRP A 373 " --> pdb=" O   SER A 369 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 47
      removed outlier: 3.564A  pdb=" N   HIS A 221 " --> pdb=" O   MET A  47 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   ALA A 269 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 134
      removed outlier: 10.294A  pdb=" N   PHE A 180 " --> pdb=" O   PRO A  96 " (cutoff:3.500A)
      removed outlier: 9.087A  pdb=" N   SER A  98 " --> pdb=" O   TYR A 178 " (cutoff:3.500A)
      removed outlier: 8.073A  pdb=" N   TYR A 178 " --> pdb=" O   SER A  98 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   HIS A 100 " --> pdb=" O   ARG A 176 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   MET A 142 " --> pdb=" O   SER A 264 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   SER A 264 " --> pdb=" O   MET A 142 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   ALA A 144 " --> pdb=" O   GLN A 262 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   GLN A 262 " --> pdb=" O   ALA A 144 " (cutoff:3.500A)
      removed outlier: 4.696A  pdb=" N   VAL A 146 " --> pdb=" O   GLU A 260 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   GLU A 260 " --> pdb=" O   VAL A 146 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   GLY A 148 " --> pdb=" O   ASN A 258 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ASN A 258 " --> pdb=" O   GLY A 148 " (cutoff:3.500A)
      removed outlier: 5.229A  pdb=" N   HIS A 150 " --> pdb=" O   CYS A 256 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   CYS A 256 " --> pdb=" O   HIS A 150 " (cutoff:3.500A)
      removed outlier: 5.251A  pdb=" N   LYS A 152 " --> pdb=" O   GLY A 254 " (cutoff:3.500A)
      removed outlier: 7.060A  pdb=" N   GLY A 254 " --> pdb=" O   LYS A 152 " (cutoff:3.500A)
      removed outlier: 5.217A  pdb=" N   ALA A 154 " --> pdb=" O   GLU A 252 " (cutoff:3.500A)
      removed outlier: 7.193A  pdb=" N   GLU A 252 " --> pdb=" O   ALA A 154 " (cutoff:3.500A)
      removed outlier: 5.375A  pdb=" N   PHE A 156 " --> pdb=" O   ALA A 250 " (cutoff:3.500A)
      removed outlier: 7.094A  pdb=" N   ALA A 250 " --> pdb=" O   PHE A 156 " (cutoff:3.500A)
      removed outlier: 5.102A  pdb=" N   ALA A 158 " --> pdb=" O   LEU A 248 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   LEU A 248 " --> pdb=" O   ALA A 158 " (cutoff:3.500A)
      removed outlier: 5.280A  pdb=" N   LYS A 160 " --> pdb=" O   ASN A 246 " (cutoff:3.500A)
      removed outlier: 7.433A  pdb=" N   ASN A 246 " --> pdb=" O   LYS A 160 " (cutoff:3.500A)
      removed outlier: 5.176A  pdb=" N   TYR A 162 " --> pdb=" O   THR A 244 " (cutoff:3.500A)
      removed outlier: 7.201A  pdb=" N   THR A 244 " --> pdb=" O   TYR A 162 " (cutoff:3.500A)
      removed outlier: 5.222A  pdb=" N   ASP A 164 " --> pdb=" O   GLN A 242 " (cutoff:3.500A)
      removed outlier: 7.162A  pdb=" N   GLN A 242 " --> pdb=" O   ASP A 164 " (cutoff:3.500A)
      removed outlier: 5.012A  pdb=" N   TYR A 166 " --> pdb=" O   THR A 240 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   THR A 240 " --> pdb=" O   TYR A 166 " (cutoff:3.500A)
      removed outlier: 5.461A  pdb=" N   PHE A 168 " --> pdb=" O   LEU A 238 " (cutoff:3.500A)
      removed outlier: 7.251A  pdb=" N   LEU A 238 " --> pdb=" O   PHE A 168 " (cutoff:3.500A)
      removed outlier: 5.407A  pdb=" N   SER A 170 " --> pdb=" O   THR A 236 " (cutoff:3.500A)
      removed outlier: 7.418A  pdb=" N   THR A 236 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 5.396A  pdb=" N   THR A 172 " --> pdb=" O   VAL A 234 " (cutoff:3.500A)
      removed outlier: 7.329A  pdb=" N   VAL A 234 " --> pdb=" O   THR A 172 " (cutoff:3.500A)
      removed outlier: 5.289A  pdb=" N   GLU A 174 " --> pdb=" O   ILE A 232 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   ILE A 232 " --> pdb=" O   GLU A 174 " (cutoff:3.500A)
      removed outlier: 5.182A  pdb=" N   ARG A 176 " --> pdb=" O   GLY A 230 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   GLY A 230 " --> pdb=" O   ARG A 176 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   SER A 341 " --> pdb=" O   THR A 224 " (cutoff:3.500A)
      removed outlier: 5.025A  pdb=" N   VAL A 226 " --> pdb=" O   ASP A 339 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   ASP A 339 " --> pdb=" O   VAL A 226 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 76
      removed outlier: 4.348A  pdb=" N   THR A  73 " --> pdb=" O   LEU A  87 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 459 through 460
      removed outlier: 4.182A  pdb=" N   PHE A 421 " --> pdb=" O   TRP A 460 " (cutoff:3.500A)
      removed outlier: 6.080A  pdb=" N   VAL A 418 " --> pdb=" O   HIS A 521 " (cutoff:3.500A)
      removed outlier: 7.322A  pdb=" N   HIS A 521 " --> pdb=" O   VAL A 418 " (cutoff:3.500A)
      removed outlier: 5.086A  pdb=" N   ASN A 420 " --> pdb=" O   SER A 519 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   SER A 519 " --> pdb=" O   ASN A 420 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 464 through 470
      removed outlier: 5.188A  pdb=" N   ASP A 465 " --> pdb=" O   VAL A 418 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   VAL A 418 " --> pdb=" O   ASP A 465 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   GLU A 467 " --> pdb=" O   LEU A 416 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   LEU A 416 " --> pdb=" O   GLU A 467 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   LYS A 523 " --> pdb=" O   HIS A 415 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 445 through 448
      removed outlier: 6.633A  pdb=" N   LEU A 477 " --> pdb=" O   ASP A 497 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   ASP A 497 " --> pdb=" O   LEU A 477 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   VAL A 479 " --> pdb=" O   SER A 495 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   SER A 495 " --> pdb=" O   VAL A 479 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   VAL A 481 " --> pdb=" O   LEU A 493 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ASP A 491 " --> pdb=" O   ASP A 483 " (cutoff:3.500A)

    143 hydrogen bonds defined for protein.
    405 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.01

  Time building geometry restraints manager: 1.15 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.19 -     1.32: 669
        1.32 -     1.45: 1180
        1.45 -     1.58: 2251
        1.58 -     1.71: 0
        1.71 -     1.84: 36
  Bond restraints: 4136
  Sorted by residual:
  bond pdb=" C7  NAG A 604 "
       pdb=" N2  NAG A 604 "
    ideal  model  delta    sigma   weight residual
    1.346  1.463 -0.117 2.00e-02 2.50e+03 3.42e+01
  bond pdb=" C1  NAG A 604 "
       pdb=" O5  NAG A 604 "
    ideal  model  delta    sigma   weight residual
    1.406  1.504 -0.098 2.00e-02 2.50e+03 2.42e+01
  bond pdb=" C5  NAG A 604 "
       pdb=" O5  NAG A 604 "
    ideal  model  delta    sigma   weight residual
    1.413  1.474 -0.061 2.00e-02 2.50e+03 9.43e+00
  bond pdb=" C2  NAG A 604 "
       pdb=" N2  NAG A 604 "
    ideal  model  delta    sigma   weight residual
    1.439  1.499 -0.060 2.00e-02 2.50e+03 9.08e+00
  bond pdb=" C3  NAG A 604 "
       pdb=" O3  NAG A 604 "
    ideal  model  delta    sigma   weight residual
    1.403  1.453 -0.050 2.00e-02 2.50e+03 6.19e+00
  ... (remaining 4131 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 5355
        1.53 -     3.06: 197
        3.06 -     4.58: 39
        4.58 -     6.11: 19
        6.11 -     7.64: 1
  Bond angle restraints: 5611
  Sorted by residual:
  angle pdb=" N   ARG A 298 "
        pdb=" CA  ARG A 298 "
        pdb=" C   ARG A 298 "
      ideal   model   delta    sigma   weight residual
     109.52  101.88    7.64 1.55e+00 4.16e-01 2.43e+01
  angle pdb=" CA  ARG A 298 "
        pdb=" C   ARG A 298 "
        pdb=" O   ARG A 298 "
      ideal   model   delta    sigma   weight residual
     121.44  116.82    4.62 1.17e+00 7.31e-01 1.56e+01
  angle pdb=" N   ASP A  82 "
        pdb=" CA  ASP A  82 "
        pdb=" C   ASP A  82 "
      ideal   model   delta    sigma   weight residual
     111.71  106.85    4.86 1.34e+00 5.57e-01 1.32e+01
  angle pdb=" N   VAL A 451 "
        pdb=" CA  VAL A 451 "
        pdb=" C   VAL A 451 "
      ideal   model   delta    sigma   weight residual
     107.37  111.93   -4.56 1.48e+00 4.57e-01 9.49e+00
  angle pdb=" C   CYS A 396 "
        pdb=" N   GLN A 397 "
        pdb=" CA  GLN A 397 "
      ideal   model   delta    sigma   weight residual
     121.54  126.90   -5.36 1.91e+00 2.74e-01 7.87e+00
  ... (remaining 5606 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.11: 2246
       17.11 -    34.22: 203
       34.22 -    51.33: 45
       51.33 -    68.44: 7
       68.44 -    85.55: 7
  Dihedral angle restraints: 2508
    sinusoidal: 1030
      harmonic: 1478
  Sorted by residual:
  dihedral pdb=" CB  CYS A 376 "
           pdb=" SG  CYS A 376 "
           pdb=" SG  CYS A 392 "
           pdb=" CB  CYS A 392 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -4.35  -81.65     1      1.00e+01 1.00e-02 8.21e+01
  dihedral pdb=" CB  CYS A 396 "
           pdb=" SG  CYS A 396 "
           pdb=" SG  CYS A 406 "
           pdb=" CB  CYS A 406 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  146.15  -53.15     1      1.00e+01 1.00e-02 3.84e+01
  dihedral pdb=" CA  LEU A 359 "
           pdb=" C   LEU A 359 "
           pdb=" N   ARG A 360 "
           pdb=" CA  ARG A 360 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.96  -26.04     0      5.00e+00 4.00e-02 2.71e+01
  ... (remaining 2505 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 370
       0.034 -    0.068: 156
       0.068 -    0.101: 48
       0.101 -    0.135: 26
       0.135 -    0.169: 4
  Chirality restraints: 604
  Sorted by residual:
  chirality pdb=" CA  ARG A 298 "
            pdb=" N   ARG A 298 "
            pdb=" C   ARG A 298 "
            pdb=" CB  ARG A 298 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.15e-01
  chirality pdb=" CA  GLU A 446 "
            pdb=" N   GLU A 446 "
            pdb=" C   GLU A 446 "
            pdb=" CB  GLU A 446 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.96e-01
  chirality pdb=" CA  ILE A 232 "
            pdb=" N   ILE A 232 "
            pdb=" C   ILE A 232 "
            pdb=" CB  ILE A 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.82e-01
  ... (remaining 601 not shown)

  Planarity restraints: 739
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 499 "    0.050 5.00e-02 4.00e+02   7.67e-02 9.42e+00
        pdb=" N   PRO A 500 "   -0.133 5.00e-02 4.00e+02
        pdb=" CA  PRO A 500 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 500 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A  95 "   -0.050 5.00e-02 4.00e+02   7.63e-02 9.32e+00
        pdb=" N   PRO A  96 "    0.132 5.00e-02 4.00e+02
        pdb=" CA  PRO A  96 "   -0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A  96 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 407 "    0.041 5.00e-02 4.00e+02   6.05e-02 5.86e+00
        pdb=" N   PRO A 408 "   -0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO A 408 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 408 "    0.034 5.00e-02 4.00e+02
  ... (remaining 736 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 184
        2.72 -     3.27: 3973
        3.27 -     3.81: 6105
        3.81 -     4.36: 6879
        4.36 -     4.90: 12259
  Nonbonded interactions: 29400
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 320 "
            pdb=" OE1 GLN A 323 "
     model   vdw
     2.177 3.040
  nonbonded pdb=" O   TYR A 366 "
            pdb=" OG  SER A 369 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" OH  TYR A 366 "
            pdb=" NH1 ARG A 370 "
     model   vdw
     2.215 3.120
  nonbonded pdb=" OE2 GLU A 395 "
            pdb=" OG  SER A 399 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" O   GLN A 361 "
            pdb=" OG  SER A 364 "
     model   vdw
     2.247 3.040
  ... (remaining 29395 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.210
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5782
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.117   4136  Z= 0.316
  Angle     :  0.746   7.641   5611  Z= 0.411
  Chirality :  0.046   0.169    604
  Planarity :  0.006   0.077    738
  Dihedral  : 13.809  85.555   1525
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.70 (0.35), residues: 505
  helix: -1.61 (0.67), residues: 55
  sheet:  0.15 (0.33), residues: 207
  loop : -2.22 (0.38), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 327 
 HIS   0.003   0.001   HIS A 292 
 PHE   0.016   0.002   PHE A 447 
 TYR   0.012   0.001   TYR A 437 
 ARG   0.006   0.001   ARG A 422 

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  214 LEU cc_start: 0.8991 (tp) cc_final: 0.8630 (mp)
REVERT: A  231 ARG cc_start: 0.7457 (ttm170) cc_final: 0.7176 (ttt180)
REVERT: A  479 VAL cc_start: 0.9503 (t) cc_final: 0.9156 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.2504
  time to fit residues: 27.8708
Evaluate side-chains
  48 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:   20.0000
   chunk 37 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   chunk 12 optimal weight:   10.0000
   chunk 25 optimal weight:    4.9990
   chunk 20 optimal weight:   10.0000
   chunk 39 optimal weight:    7.9990
   chunk 15 optimal weight:    6.9990
   chunk 23 optimal weight:    5.9990
   chunk 29 optimal weight:    8.9990
   chunk 45 optimal weight:    7.9990
   overall best weight:    5.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 212 HIS
A 285 HIS
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 375 ASN
** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 539 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5507 r_free = 0.5507 target = 0.362890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.5401 r_free = 0.5401 target = 0.194882 restraints weight = 4445.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.5358 r_free = 0.5358 target = 0.176652 restraints weight = 7023.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 75)----------------|
| r_work = 0.5356 r_free = 0.5356 target = 0.168443 restraints weight = 5614.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.5044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6695
moved from start:          0.4857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.078   4136  Z= 0.564
  Angle     :  1.020  10.183   5611  Z= 0.559
  Chirality :  0.055   0.230    604
  Planarity :  0.009   0.091    738
  Dihedral  :  7.270  28.357    579
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 23.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.11 %
    Favored  : 90.89 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 10.96 %
    Favored  : 85.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.21 (0.35), residues: 505
  helix:  0.06 (0.72), residues: 51
  sheet: -2.44 (0.32), residues: 206
  loop : -2.25 (0.38), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.003   TRP A 128 
 HIS   0.014   0.003   HIS A 292 
 PHE   0.037   0.003   PHE A 156 
 TYR   0.020   0.003   TYR A 275 
 ARG   0.009   0.001   ARG A 360 

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 66
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 TYR cc_start: 0.7306 (p90) cc_final: 0.6996 (p90)
REVERT: A  128 TRP cc_start: 0.6508 (m100) cc_final: 0.6305 (m-10)
REVERT: A  163 GLN cc_start: 0.8044 (pt0) cc_final: 0.7712 (tm-30)
REVERT: A  174 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6987 (mp0)
REVERT: A  279 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7746 (mp0)
REVERT: A  293 GLN cc_start: 0.7388 (OUTLIER) cc_final: 0.7101 (mp10)
REVERT: A  343 GLU cc_start: 0.8688 (tp30) cc_final: 0.8442 (tp30)
REVERT: A  464 MET cc_start: 0.7448 (tpp) cc_final: 0.7186 (tpp)
  outliers start: 14
  outliers final: 10
  residues processed: 78
  average time/residue: 0.1862
  time to fit residues: 18.0765
Evaluate side-chains
  57 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 TYR
Chi-restraints excluded: chain A residue  169 ASN
Chi-restraints excluded: chain A residue  171 ASP
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  255 ASP
Chi-restraints excluded: chain A residue  293 GLN
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  516 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 5 optimal weight:    9.9990
   chunk 13 optimal weight:    8.9990
   chunk 7 optimal weight:    7.9990
   chunk 6 optimal weight:    6.9990
   chunk 17 optimal weight:    5.9990
   chunk 29 optimal weight:    9.9990
   chunk 49 optimal weight:    9.9990
   chunk 12 optimal weight:    8.9990
   overall best weight:    4.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5464 r_free = 0.5464 target = 0.357987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.5339 r_free = 0.5339 target = 0.188288 restraints weight = 4442.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.5310 r_free = 0.5310 target = 0.178241 restraints weight = 6978.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.5308 r_free = 0.5308 target = 0.175007 restraints weight = 5679.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.5033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6724
moved from start:          0.6165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.059   4136  Z= 0.452
  Angle     :  0.982  10.996   5611  Z= 0.532
  Chirality :  0.053   0.184    604
  Planarity :  0.007   0.055    738
  Dihedral  :  7.243  31.074    579
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 22.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.08 %
    Favored  : 87.92 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 15.98 %
    Favored  : 79.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.74 (0.34), residues: 505
  helix: -0.88 (0.65), residues: 58
  sheet: -3.02 (0.32), residues: 206
  loop : -2.24 (0.37), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP A 128 
 HIS   0.014   0.002   HIS A 285 
 PHE   0.032   0.003   PHE A 156 
 TYR   0.029   0.003   TYR A 166 
 ARG   0.007   0.001   ARG A 360 

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 56
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  163 GLN cc_start: 0.8060 (pt0) cc_final: 0.7350 (tm-30)
REVERT: A  169 ASN cc_start: 0.8731 (OUTLIER) cc_final: 0.8228 (p0)
REVERT: A  174 GLU cc_start: 0.7394 (mt-10) cc_final: 0.6922 (mp0)
REVERT: A  279 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7454 (mp0)
REVERT: A  372 ARG cc_start: 0.7652 (ppt170) cc_final: 0.7313 (ppt170)
REVERT: A  464 MET cc_start: 0.7472 (tpp) cc_final: 0.6785 (tpp)
REVERT: A  477 LEU cc_start: 0.9191 (tt) cc_final: 0.8868 (mt)
REVERT: A  488 TRP cc_start: 0.5045 (p90) cc_final: 0.3299 (t60)
  outliers start: 18
  outliers final: 9
  residues processed: 68
  average time/residue: 0.1933
  time to fit residues: 16.1393
Evaluate side-chains
  54 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 44
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 TYR
Chi-restraints excluded: chain A residue  169 ASN
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  360 ARG
Chi-restraints excluded: chain A residue  516 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 16 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   chunk 24 optimal weight:    0.4980
   chunk 41 optimal weight:    1.9990
   chunk 42 optimal weight:   20.0000
   chunk 13 optimal weight:    3.9990
   chunk 40 optimal weight:    8.9990
   chunk 12 optimal weight:   20.0000
   overall best weight:    1.2986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 397 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5505 r_free = 0.5505 target = 0.371325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.5457 r_free = 0.5457 target = 0.237485 restraints weight = 4395.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.5459 r_free = 0.5459 target = 0.194911 restraints weight = 4762.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.5454 r_free = 0.5454 target = 0.181595 restraints weight = 4347.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.5102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6589
moved from start:          0.6307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   4136  Z= 0.235
  Angle     :  0.775   9.472   5611  Z= 0.407
  Chirality :  0.050   0.313    604
  Planarity :  0.005   0.050    738
  Dihedral  :  5.642  19.950    579
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 15.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.12 %
    Favored  : 91.88 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 18.04 %
    Favored  : 79.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.14 (0.35), residues: 505
  helix: -0.61 (0.68), residues: 58
  sheet: -2.36 (0.34), residues: 191
  loop : -2.15 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A 482 
 HIS   0.004   0.001   HIS A 513 
 PHE   0.020   0.002   PHE A 156 
 TYR   0.013   0.002   TYR A 166 
 ARG   0.006   0.001   ARG A 360 

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 48
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
REVERT: A   70 ARG cc_start: 0.5953 (tmt170) cc_final: 0.5065 (ttp80)
REVERT: A   81 ARG cc_start: 0.8180 (tpt90) cc_final: 0.7961 (mmm160)
REVERT: A  128 TRP cc_start: 0.6889 (m-90) cc_final: 0.6403 (m-10)
REVERT: A  169 ASN cc_start: 0.8143 (p0) cc_final: 0.7839 (p0)
REVERT: A  174 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6823 (mp0)
REVERT: A  279 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7643 (tt0)
REVERT: A  464 MET cc_start: 0.7372 (tpp) cc_final: 0.6631 (tpp)
REVERT: A  477 LEU cc_start: 0.9175 (tt) cc_final: 0.8825 (mt)
REVERT: A  488 TRP cc_start: 0.5247 (p90) cc_final: 0.3459 (t60)
REVERT: A  490 ASP cc_start: 0.3368 (OUTLIER) cc_final: 0.3043 (t0)
  outliers start: 9
  outliers final: 3
  residues processed: 54
  average time/residue: 0.1963
  time to fit residues: 13.0471
Evaluate side-chains
  45 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 40
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 GLU
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  490 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 4 optimal weight:    6.9990
   chunk 9 optimal weight:    4.9990
   chunk 6 optimal weight:    9.9990
   chunk 44 optimal weight:   10.0000
   chunk 49 optimal weight:    7.9990
   chunk 7 optimal weight:    9.9990
   chunk 23 optimal weight:    5.9990
   chunk 37 optimal weight:    8.9990
   chunk 40 optimal weight:    9.9990
   chunk 30 optimal weight:    6.9990
   overall best weight:    5.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 397 GLN
A 415 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5423 r_free = 0.5423 target = 0.352156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.5282 r_free = 0.5282 target = 0.176109 restraints weight = 4625.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.5245 r_free = 0.5245 target = 0.167980 restraints weight = 7658.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 70)----------------|
| r_work = 0.5240 r_free = 0.5240 target = 0.160541 restraints weight = 7396.777|
|-----------------------------------------------------------------------------|
r_work (final): 0.4969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6815
moved from start:          0.7289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.060   4136  Z= 0.532
  Angle     :  1.078  15.652   5611  Z= 0.587
  Chirality :  0.054   0.209    604
  Planarity :  0.007   0.052    738
  Dihedral  :  7.554  32.754    579
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 27.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.07 %
    Favored  : 86.93 %
  Rotamer:
    Outliers :  7.76 %
    Allowed  : 16.44 %
    Favored  : 75.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.95 (0.34), residues: 505
  helix: -1.06 (0.63), residues: 64
  sheet: -3.26 (0.32), residues: 199
  loop : -2.35 (0.37), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP A 482 
 HIS   0.014   0.003   HIS A 285 
 PHE   0.026   0.003   PHE A 156 
 TYR   0.035   0.003   TYR A 162 
 ARG   0.007   0.001   ARG A  70 

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 42
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
REVERT: A   70 ARG cc_start: 0.5804 (tmt170) cc_final: 0.4929 (ttp80)
REVERT: A  169 ASN cc_start: 0.8701 (p0) cc_final: 0.8334 (p0)
REVERT: A  235 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7750 (mp)
REVERT: A  262 GLN cc_start: 0.7288 (OUTLIER) cc_final: 0.6686 (mp10)
REVERT: A  293 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7445 (mp10)
REVERT: A  477 LEU cc_start: 0.9175 (tt) cc_final: 0.8823 (mt)
REVERT: A  488 TRP cc_start: 0.5879 (p90) cc_final: 0.3305 (t60)
REVERT: A  490 ASP cc_start: 0.3265 (OUTLIER) cc_final: 0.2559 (t0)
  outliers start: 34
  outliers final: 21
  residues processed: 68
  average time/residue: 0.1808
  time to fit residues: 15.1961
Evaluate side-chains
  64 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 39
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 MET
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  119 GLU
Chi-restraints excluded: chain A residue  123 ASN
Chi-restraints excluded: chain A residue  162 TYR
Chi-restraints excluded: chain A residue  171 ASP
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  191 ASP
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  255 ASP
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  262 GLN
Chi-restraints excluded: chain A residue  285 HIS
Chi-restraints excluded: chain A residue  293 GLN
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  490 ASP
Chi-restraints excluded: chain A residue  516 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 44 optimal weight:    7.9990
   chunk 16 optimal weight:   10.0000
   chunk 47 optimal weight:    8.9990
   chunk 39 optimal weight:   20.0000
   chunk 43 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 12 optimal weight:   10.0000
   chunk 46 optimal weight:    8.9990
   chunk 23 optimal weight:    2.9990
   chunk 40 optimal weight:    6.9990
   overall best weight:    4.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 397 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5417 r_free = 0.5417 target = 0.352399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.5302 r_free = 0.5302 target = 0.207080 restraints weight = 4493.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.5260 r_free = 0.5260 target = 0.177599 restraints weight = 6337.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 72)----------------|
| r_work = 0.5245 r_free = 0.5245 target = 0.162434 restraints weight = 6381.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.4995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6834
moved from start:          0.7646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.045   4136  Z= 0.455
  Angle     :  1.058  19.745   5611  Z= 0.572
  Chirality :  0.058   0.427    604
  Planarity :  0.007   0.054    738
  Dihedral  :  7.477  32.066    579
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 24.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.87 %
    Favored  : 87.13 %
  Rotamer:
    Outliers :  6.85 %
    Allowed  : 18.04 %
    Favored  : 75.11 %
  Cbeta Deviations :  0.42 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.25 (0.33), residues: 505
  helix: -1.53 (0.55), residues: 71
  sheet: -3.34 (0.31), residues: 208
  loop : -2.52 (0.38), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 482 
 HIS   0.012   0.002   HIS A 285 
 PHE   0.027   0.003   PHE A 156 
 TYR   0.023   0.003   TYR A 275 
 ARG   0.006   0.001   ARG A  70 

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 47
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7492 (ptm160)
REVERT: A  177 MET cc_start: 0.7717 (mmm) cc_final: 0.7434 (mmm)
REVERT: A  235 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7775 (mp)
REVERT: A  262 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.6776 (mp10)
REVERT: A  292 HIS cc_start: 0.7828 (OUTLIER) cc_final: 0.7572 (t-170)
REVERT: A  293 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7347 (mp10)
REVERT: A  477 LEU cc_start: 0.9219 (tt) cc_final: 0.8895 (mt)
REVERT: A  488 TRP cc_start: 0.5860 (p90) cc_final: 0.3360 (t60)
REVERT: A  490 ASP cc_start: 0.3457 (OUTLIER) cc_final: 0.2648 (t0)
  outliers start: 30
  outliers final: 15
  residues processed: 71
  average time/residue: 0.2308
  time to fit residues: 20.0168
Evaluate side-chains
  59 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 38
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue   98 SER
Chi-restraints excluded: chain A residue  119 GLU
Chi-restraints excluded: chain A residue  123 ASN
Chi-restraints excluded: chain A residue  129 ARG
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  262 GLN
Chi-restraints excluded: chain A residue  285 HIS
Chi-restraints excluded: chain A residue  292 HIS
Chi-restraints excluded: chain A residue  293 GLN
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  490 ASP
Chi-restraints excluded: chain A residue  516 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 7 optimal weight:    9.9990
   chunk 46 optimal weight:    4.9990
   chunk 20 optimal weight:    7.9990
   chunk 16 optimal weight:    3.9990
   chunk 9 optimal weight:    0.6980
   chunk 25 optimal weight:    7.9990
   chunk 29 optimal weight:    0.9990
   chunk 0 optimal weight:    9.9990
   chunk 18 optimal weight:   10.0000
   chunk 10 optimal weight:    0.7980
   overall best weight:    1.8986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5444 r_free = 0.5444 target = 0.361704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.5375 r_free = 0.5375 target = 0.227433 restraints weight = 4448.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.5336 r_free = 0.5336 target = 0.182393 restraints weight = 5069.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 97)----------------|
| r_work = 0.5323 r_free = 0.5323 target = 0.168722 restraints weight = 4133.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.5032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6740
moved from start:          0.7550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4136  Z= 0.275
  Angle     :  1.053  35.218   5611  Z= 0.533
  Chirality :  0.057   0.575    604
  Planarity :  0.005   0.056    738
  Dihedral  :  6.218  30.426    579
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 15.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.50 %
    Favored  : 90.50 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 20.78 %
    Favored  : 75.57 %
  Cbeta Deviations :  0.21 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.51 (0.34), residues: 505
  helix: -0.72 (0.61), residues: 64
  sheet: -2.84 (0.33), residues: 198
  loop : -2.19 (0.37), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 128 
 HIS   0.005   0.001   HIS A 285 
 PHE   0.024   0.002   PHE A 518 
 TYR   0.010   0.002   TYR A 275 
 ARG   0.004   0.000   ARG A  81 

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 42
  time to evaluate  : 0.530 
Fit side-chains
REVERT: A   45 GLU cc_start: 0.8252 (tt0) cc_final: 0.8046 (tm-30)
REVERT: A  128 TRP cc_start: 0.6509 (m-90) cc_final: 0.6286 (m-10)
REVERT: A  293 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.7251 (mp10)
REVERT: A  477 LEU cc_start: 0.9202 (tt) cc_final: 0.8886 (mt)
REVERT: A  488 TRP cc_start: 0.5919 (p90) cc_final: 0.3579 (t60)
REVERT: A  490 ASP cc_start: 0.3080 (OUTLIER) cc_final: 0.2713 (t0)
  outliers start: 16
  outliers final: 9
  residues processed: 55
  average time/residue: 0.2526
  time to fit residues: 17.5671
Evaluate side-chains
  48 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 37
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   98 SER
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  255 ASP
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  293 GLN
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  490 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 44 optimal weight:    0.0870
   chunk 40 optimal weight:   10.0000
   chunk 36 optimal weight:   10.0000
   chunk 5 optimal weight:    7.9990
   chunk 24 optimal weight:    0.0980
   chunk 7 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 16 optimal weight:   10.0000
   chunk 4 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   overall best weight:    1.6364

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5460 r_free = 0.5460 target = 0.364228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.5409 r_free = 0.5409 target = 0.241258 restraints weight = 4365.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.5378 r_free = 0.5378 target = 0.183454 restraints weight = 4669.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 77)----------------|
| r_work = 0.5363 r_free = 0.5363 target = 0.173663 restraints weight = 4519.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.5056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6659
moved from start:          0.7578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   4136  Z= 0.243
  Angle     :  1.035  33.440   5611  Z= 0.516
  Chirality :  0.053   0.442    604
  Planarity :  0.005   0.056    738
  Dihedral  :  5.799  30.677    579
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 14.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 21.23 %
    Favored  : 75.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.19 (0.35), residues: 505
  helix: -0.90 (0.62), residues: 64
  sheet: -2.36 (0.34), residues: 198
  loop : -2.12 (0.37), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.003   TRP A 482 
 HIS   0.005   0.001   HIS A 285 
 PHE   0.017   0.002   PHE A 168 
 TYR   0.016   0.002   TYR A 536 
 ARG   0.007   0.001   ARG A 213 

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 43
  time to evaluate  : 0.575 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 GLU cc_start: 0.8408 (tm-30) cc_final: 0.7804 (tm-30)
REVERT: A  128 TRP cc_start: 0.6365 (m-90) cc_final: 0.6157 (m-10)
REVERT: A  177 MET cc_start: 0.7685 (mmm) cc_final: 0.7418 (mmm)
REVERT: A  477 LEU cc_start: 0.9234 (tt) cc_final: 0.8920 (mt)
REVERT: A  488 TRP cc_start: 0.5855 (p90) cc_final: 0.3803 (t60)
REVERT: A  490 ASP cc_start: 0.3263 (OUTLIER) cc_final: 0.2622 (t0)
  outliers start: 13
  outliers final: 9
  residues processed: 54
  average time/residue: 0.1943
  time to fit residues: 13.4178
Evaluate side-chains
  52 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 42
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   98 SER
Chi-restraints excluded: chain A residue  162 TYR
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  255 ASP
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  490 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 31 optimal weight:    0.0980
   chunk 26 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 5 optimal weight:   10.0000
   chunk 36 optimal weight:   10.0000
   chunk 19 optimal weight:    7.9990
   chunk 6 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 3 optimal weight:    5.9990
   chunk 47 optimal weight:    5.9990
   overall best weight:    2.3986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 397 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5440 r_free = 0.5440 target = 0.360608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.5371 r_free = 0.5371 target = 0.228375 restraints weight = 4393.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.5371 r_free = 0.5371 target = 0.195447 restraints weight = 5025.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.5361 r_free = 0.5361 target = 0.187580 restraints weight = 6038.452|
|-----------------------------------------------------------------------------|
r_work (final): 0.5081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6615
moved from start:          0.7828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4136  Z= 0.285
  Angle     :  1.023  29.435   5611  Z= 0.515
  Chirality :  0.055   0.494    604
  Planarity :  0.005   0.047    738
  Dihedral  :  6.113  29.050    579
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 15.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.69 %
    Favored  : 89.31 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 21.00 %
    Favored  : 76.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.22 (0.35), residues: 505
  helix: -0.76 (0.62), residues: 64
  sheet: -2.42 (0.34), residues: 198
  loop : -2.16 (0.37), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP A 482 
 HIS   0.008   0.001   HIS A 285 
 PHE   0.024   0.002   PHE A 518 
 TYR   0.024   0.002   TYR A 536 
 ARG   0.007   0.001   ARG A 213 

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 44
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 TRP cc_start: 0.6454 (m-90) cc_final: 0.6203 (m-10)
REVERT: A  276 LYS cc_start: 0.8669 (mttt) cc_final: 0.7730 (tmtt)
REVERT: A  477 LEU cc_start: 0.9189 (tt) cc_final: 0.8936 (mt)
REVERT: A  488 TRP cc_start: 0.5993 (p90) cc_final: 0.3870 (t60)
REVERT: A  490 ASP cc_start: 0.3275 (OUTLIER) cc_final: 0.2613 (t0)
  outliers start: 12
  outliers final: 10
  residues processed: 54
  average time/residue: 0.1818
  time to fit residues: 12.3516
Evaluate side-chains
  53 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   98 SER
Chi-restraints excluded: chain A residue  162 TYR
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  255 ASP
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  490 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    0.0970
   chunk 48 optimal weight:    7.9990
   chunk 24 optimal weight:    0.1980
   chunk 39 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 6 optimal weight:    6.9990
   chunk 38 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 30 optimal weight:    0.1980
   chunk 37 optimal weight:   10.0000
   chunk 44 optimal weight:    9.9990
   overall best weight:    1.2982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 397 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5461 r_free = 0.5461 target = 0.368372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.5423 r_free = 0.5423 target = 0.248748 restraints weight = 4373.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.5416 r_free = 0.5416 target = 0.190131 restraints weight = 4513.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 75)----------------|
| r_work = 0.5401 r_free = 0.5401 target = 0.181528 restraints weight = 5108.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.5085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6619
moved from start:          0.7790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4136  Z= 0.215
  Angle     :  0.966  28.242   5611  Z= 0.480
  Chirality :  0.053   0.453    604
  Planarity :  0.005   0.049    738
  Dihedral  :  5.544  27.785    579
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.12 %
    Favored  : 91.88 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 21.92 %
    Favored  : 76.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.97 (0.35), residues: 505
  helix: -0.71 (0.64), residues: 64
  sheet: -2.05 (0.35), residues: 191
  loop : -2.17 (0.37), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.003   TRP A 482 
 HIS   0.004   0.001   HIS A 285 
 PHE   0.016   0.002   PHE A 156 
 TYR   0.031   0.002   TYR A 536 
 ARG   0.008   0.001   ARG A 213 

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 41
  time to evaluate  : 0.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 MET cc_start: 0.7829 (mmm) cc_final: 0.7517 (mmm)
REVERT: A  477 LEU cc_start: 0.9197 (tt) cc_final: 0.8910 (mt)
REVERT: A  488 TRP cc_start: 0.5951 (p90) cc_final: 0.3752 (t60)
  outliers start: 8
  outliers final: 8
  residues processed: 48
  average time/residue: 0.2389
  time to fit residues: 14.6498
Evaluate side-chains
  47 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue  162 TYR
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  255 ASP
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  438 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 6 optimal weight:   20.0000
   chunk 11 optimal weight:    0.1980
   chunk 41 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   chunk 40 optimal weight:   10.0000
   chunk 19 optimal weight:    4.9990
   chunk 42 optimal weight:   20.0000
   chunk 5 optimal weight:    6.9990
   chunk 3 optimal weight:   10.0000
   overall best weight:    2.6388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 397 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5439 r_free = 0.5439 target = 0.360546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.5379 r_free = 0.5379 target = 0.236552 restraints weight = 4403.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.5334 r_free = 0.5334 target = 0.177635 restraints weight = 4814.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.5322 r_free = 0.5322 target = 0.173459 restraints weight = 5353.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.5045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6704
moved from start:          0.7983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4136  Z= 0.291
  Angle     :  1.015  28.153   5611  Z= 0.512
  Chirality :  0.054   0.441    604
  Planarity :  0.005   0.045    738
  Dihedral  :  6.193  25.036    579
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 16.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.10 %
    Favored  : 89.90 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 21.00 %
    Favored  : 76.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.09 (0.35), residues: 505
  helix: -0.56 (0.65), residues: 64
  sheet: -2.37 (0.34), residues: 203
  loop : -2.05 (0.38), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A 482 
 HIS   0.009   0.001   HIS A 189 
 PHE   0.026   0.002   PHE A 518 
 TYR   0.026   0.002   TYR A 536 
 ARG   0.008   0.001   ARG A 213 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1852.54 seconds
wall clock time: 33 minutes 54.13 seconds (2034.13 seconds total)